Metroid Prime Trilogy pre-existing save

I played through the entirety of mp1 and about half of mp2 a couple years back. Then I started putting my backups on a new drive and only now have re-installed the trilogy. I remember having to use an alt dol before and being able to save and resume my games. I'm having trouble with that now. My saves are still there but the alt dols that I have available to me within configurable usb loader all boot me directly into the individual games with no option to load a save. I feel like I'm forgetting something. How do I resume my old saved games?

I just remembered that I was playing the game from a burned backup. Now, I'm using a usb loader. So I guess my question now is: What is the best way to enjoy mp trilogy via usb loader? (I have the one with the third game removed...)